Chloroplast Genome Analysis of Two Medicinal <i>Coelogyne</i> spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

• Main Authors: Kai Jiang, Li-Yuan Miao, Zheng-Wei Wang, Zi-Yi Ni, Chao Hu, Xin-Hua Zeng, Wei-Chang Huang
• Format: Article
• Language: English
• Published: MDPI AG 2020-10-01
• Series: Plants
• Subjects: Coelogyne; chloroplast genome; phylogeny; molecular identification
• Online Access: https://www.mdpi.com/2223-7747/9/10/1332

Although the medicinal properties of <i>Coelogyne</i> spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used<b> </b>the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of <i>Coelogyne</i><i> fimbriata</i> and <i>Coelogyne</i><i> ovalis</i>. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two <i>Coelogyne</i> species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16<i> </i><i>Coelogyne</i> species. We constructed phylogenetic trees including 18 <i>Coelogyne</i> species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of <i>C. fimbriata</i> and <i>C. ovalis</i> contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in <i>C. fimbriata</i> and 26,715 bp <i>C. ovalis</i>, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera <i>Coelogyne</i> and <i>Pleione</i>. The newly developed primers revealed good transferability among the <i>Coelogyne</i> taxa and provided enough variable sites to distinguish <i>C. fimbriata</i> and <i>C. ovalis</i>. The two complete cp genomes and the eight new primers of <i>Coelogyne</i> provide new genomic data for<b> </b>further studies on phylogenomics, population genetics, and evolutionary history of <i>Coelogyne</i> taxa.